The printer cannot possibly know where the centre of your bed is. All it knows is the home position (determined by the location of your endstops), the maximum x, y, and z ranges in mm, and also how many steps it needs to turn the motors to produce a mm of travel.
So you just need to go to firmware and enter the correct
#define X_MAX_POS
(and simly for Y and Z)
and
#define DEFAULT_AXIS_STEPS_PER_UNIT
following the guide pointed out above.
It may be that you have already the correct steps/mm, but if your max ranges are not correct then it won't centre where you expect it to.